My suggestion on the roof area is to check out [url]www.Buildingscience.com. Any cathedral questions can be answered there. As for the other questions there are variables to answer such as, does your basement or crawlspace have a concrete floor with a vapor barrier.Baths and dryers vented outside. Insulation in the walls? Type? The siding you are talking about can trap moisture.
What was causing the decay in the first place?
Any more elaboration is helpful for all of us.